Wiki source code of Creating particle recognition training data for deep learning
Last modified by hajaalin@helsinki_fi on 2024/01/24 07:08
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1 | (Thanks to Piotr Chmielarz for this info and for pioneering deep-learning approach at the Viikki Campus) | ||
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3 | = Description of Training data = | ||
4 | |||
5 | The training data consists of 1) original data and 2) annotations as binary images with a single white pixel indicating the center of the particle. Other indications: | ||
6 | |||
7 | * All images the same size. | ||
8 | * Even image size. | ||
9 | * Not too big images, 400 x 400 is still good. | ||
10 | * All particles in the image must be annotated. | ||
11 | * 8-bit binary images. | ||
12 | * Include also difficult cases in the training set. | ||
13 | * Save original and annotation with the same name in different folders | ||
14 | ** training_data/originals/image2.tiff | ||
15 | ** training_data/annotations/image2.tiff | ||
16 | |||
17 | = Creating the training data set with Fiji = | ||
18 | |||
19 | 1. Open original file (File → Open...). | ||
20 | 1. Duplicate original file (Image → Duplicate...). | ||
21 | 1. Close original file. | ||
22 | 1. Crop duplicate to 400 x 400 or smaller. | ||
23 | 11. Open macro editor (File → New → Script). | ||
24 | 11. Set language to ImageJ macro language (Language → IJ1 macro). | ||
25 | 11. Type in editor screen "makeRectangle(50, 50, 400, 400);" (without the "s). | ||
26 | 11. Click "Run". | ||
27 | 11. Select the image window and verify that a rectangular selection was created. | ||
28 | 11. Drag the selection to a good location on the image. | ||
29 | 11. Crop (Image → Crop). | ||
30 | 1. Create multi-point selection. | ||
31 | 11. Select multi-point tool. | ||
32 | 11. Click on particle centers. | ||
33 | 1. Create a blank annotation image. | ||
34 | 11. Duplicate cropped image (Image → Duplicate). | ||
35 | 11. Edit → Selection → Select all. | ||
36 | 11. Edit → Clear. | ||
37 | 11. Image → Type → 8-bit. | ||
38 | 1. Transfer annotations. | ||
39 | 11. Select the image with particles selected | ||
40 | 11. Edit → Selection → Add to Manager. | ||
41 | 11. Select the blank image. | ||
42 | 11. Select ROI Manager, click on the point set. | ||
43 | 1. Draw pixels. | ||
44 | 11. Select the blank images (now with particle centers) | ||
45 | 11. Edit → Draw. | ||
46 | 1. Save files (File → Save as... → TIFF) | ||
47 | |||
48 | \\ | ||
49 | |||
50 | \\ |